nextpresso implements a pipeline to perform a complete analysis of RNA-seq data, across four different execution levels:

(1) read quality and contamination checks
(2) read preprocessing through read trimming and/or down-sampling
(3) aligning of reads to the genomic reference
(4) processing of the alignment files to perform different analysis: fusion search, quantification and diff. exp. with HTseq-count and DESeq2, quantification and diff. exp. with Cuffnorm/Cuffdiff, generation of bigwig files for genome browsers, Gene set enrichment analysis with GSEApreranked

nextpresso can be executed on HPC (SGE or PBS queue systems), although sequential execution in a single workstation is also allowed.
O. Graņa; M. Rubio-Camarillo; F. Fdez-Riverola; D.G. Pisano; D. Glez-Peņa (2017) nextpresso: next generation sequencing expression analysis pipeline. Current Bioinformatics. Volume 13, Issue 6:583-591. DOI: 10.2174/1574893612666170810153850                                                                                         

nextpresso tutorial
Download nextpresso from GitHub
Download nextpresso docker image from Docker Hub
Osvaldo Graña
Miriam Rubio-Camarillo
F. Fdez-Riverola
David G. Pisano
D. Glez-Peña